# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:45:40 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-methoxy-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]quinoline-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](OCc2ccc3ccc(cc3n2)C(O)=O)[C@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 R8B  R8B  '2-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-methoxy-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]quinoline-7-carboxylic acid'  ligand  47  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R8B
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 R8B  O7   O  O      0  -0.584   4.8261  -0.0064   7.1474
 R8B  C17  C  C      0   0.403   5.7886  -0.5558   7.7157
 R8B  O6   O  OC    -1  -0.581   6.4061  -0.1510   8.7176
 R8B  C15  C  CR6    0  -0.103   6.2627  -1.8788   7.1127
 R8B  C14  C  CR16   0  -0.289   5.6072  -2.4281   5.9867
 R8B  C13  C  CR16   0  -0.305   6.0133  -3.6154   5.4405
 R8B  C11  C  CR66   0   0.070   7.1036  -4.3188   5.9938
 R8B  C10  C  CR16   0  -0.182   7.5731  -5.5512   5.4854
 R8B  C9   C  CR16   0  -0.321   8.6334  -6.1585   6.0857
 R8B  C16  C  CR16   0  -0.356   7.3283  -2.5538   7.6564
 R8B  C12  C  CR66   0   0.219   7.7727  -3.7786   7.1166
 R8B  N    N  N      0  -0.450   8.8313  -4.4011   7.6984
 R8B  C8   C  CR6    0   0.162   9.2402  -5.5347   7.2062
 R8B  C7   C  CH2    0  -0.187  10.4091  -6.2454   7.8304
 R8B  O3   O  O2     0  -0.490  10.9218  -5.5221   8.9122
 R8B  C2   C  CH1    0  -0.009  12.0169  -6.1427   9.5469
 R8B  C1   C  CH1    0  -0.007  13.3185  -5.8746   8.7837
 R8B  O4   O  OH1    0  -0.666  13.5092  -4.5000   8.5652
 R8B  C3   C  CH1    0  -0.016  12.1079  -5.6089  10.9684
 R8B  O2   O  OH1    0  -0.660  10.9509  -6.0038  11.6599
 R8B  C4   C  CH1    0   0.271  13.3628  -6.2024  11.6293
 R8B  O1   O  O2     0  -0.492  13.5405  -5.7986  12.9410
 R8B  C6   C  CH3    0  -0.423  13.8441  -4.4333  13.1704
 R8B  O    O  O2     0  -0.497  14.5089  -5.8865  10.8911
 R8B  C    C  CH1    0  -0.003  14.4905  -6.4241   9.5860
 R8B  C5   C  CH2    0  -0.155  15.8239  -6.1397   8.9272
 R8B  O5   O  OH1    0  -0.666  16.8252  -6.8609   9.6046
 R8B  H2   H  HCR6   0   0.245   4.7706  -1.8943   5.5575
 R8B  H3   H  HCR6   0   0.252   5.5026  -4.0289   4.5785
 R8B  H4   H  HCR6   0   0.266   7.0863  -5.9985   4.6270
 R8B  H5   H  HCR6   0   0.266   9.0186  -7.1024   5.7202
 R8B  H6   H  HCR6   0   0.241   7.8495  -2.1548   8.5172
 R8B  H7   H  HCH2   0   0.239  10.0824  -7.2468   8.1478
 R8B  H8   H  HCH2   0   0.235  11.1622  -6.4087   7.0465
 R8B  H9   H  HCH1   0   0.229  11.8669  -7.2333   9.5942
 R8B  H10  H  HCH1   0   0.233  13.2928  -6.4278   7.8327
 R8B  H11  H  HOH1   0   0.450  12.6942  -4.1411   8.1966
 R8B  H12  H  HCH1   0   0.226  12.1967  -4.5144  10.9234
 R8B  H13  H  HOH1   0   0.452  10.9647  -5.6018  12.5342
 R8B  H14  H  HCH1   0   0.220  13.2330  -7.2965  11.6826
 R8B  H15  H  HCH3   0   0.237  13.8308  -4.2924  14.2495
 R8B  H16  H  HCH3   0   0.223  14.8335  -4.1599  12.7992
 R8B  H17  H  HCH3   0   0.216  13.1102  -3.7509  12.7340
 R8B  H18  H  HCH1   0   0.228  14.3557  -7.5175   9.6333
 R8B  H19  H  HCH2   0   0.201  15.7478  -6.4407   7.8739
 R8B  H20  H  HCH2   0   0.208  16.0204  -5.0618   8.9415
 R8B  H21  H  HOH1   0   0.454  17.6777  -6.5917   9.2509

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 R8B  C13  C14  aromatic  1.369  0.020  1.369
 R8B  C13  C11  aromatic  1.411  0.020  1.411
 R8B  C14  C15  aromatic  1.414  0.020  1.414
 R8B  C10  C11  aromatic  1.413  0.020  1.413
 R8B  C10  C9   aromatic  1.361  0.020  1.361
 R8B  C11  C12  aromatic  1.414  0.020  1.414
 R8B  C9   C8   aromatic  1.419  0.020  1.419
 R8B  C15  C17  single    1.529  0.020  1.529
 R8B  C15  C16  aromatic  1.374  0.020  1.374
 R8B  C12  C16  aromatic  1.410  0.020  1.410
 R8B  C12  N    aromatic  1.359  0.020  1.359
 R8B  C17  O7   deloc     1.246  0.020  1.246
 R8B  C17  O6   deloc     1.245  0.020  1.245
 R8B  C8   N    aromatic  1.302  0.020  1.302
 R8B  C8   C7   single    1.504  0.020  1.504
 R8B  C7   O3   single    1.399  0.020  1.399
 R8B  O4   C1   single    1.405  0.020  1.405
 R8B  C1   C    single    1.523  0.020  1.523
 R8B  C1   C2   single    1.532  0.020  1.532
 R8B  C5   C    single    1.514  0.020  1.514
 R8B  C5   O5   single    1.408  0.020  1.408
 R8B  O3   C2   single    1.410  0.020  1.410
 R8B  C    O    single    1.412  0.020  1.412
 R8B  C2   C3   single    1.521  0.020  1.521
 R8B  O    C4   single    1.399  0.020  1.399
 R8B  C3   C4   single    1.537  0.020  1.537
 R8B  C3   O2   single    1.405  0.020  1.405
 R8B  C4   O1   single    1.384  0.020  1.384
 R8B  O1   C6   single    1.417  0.020  1.417
 R8B  C14  H2   single    0.930  0.020  1.080
 R8B  C13  H3   single    0.930  0.020  1.080
 R8B  C10  H4   single    0.930  0.020  1.080
 R8B  C9   H5   single    0.930  0.020  1.080
 R8B  C16  H6   single    0.930  0.020  1.080
 R8B  C7   H7   single    0.970  0.020  1.090
 R8B  C7   H8   single    0.970  0.020  1.090
 R8B  C2   H9   single    0.970  0.020  1.090
 R8B  C1   H10  single    0.970  0.020  1.090
 R8B  O4   H11  single    0.850  0.020  0.980
 R8B  C3   H12  single    0.970  0.020  1.090
 R8B  O2   H13  single    0.850  0.020  0.980
 R8B  C4   H14  single    0.970  0.020  1.090
 R8B  C6   H15  single    0.970  0.020  1.090
 R8B  C6   H16  single    0.970  0.020  1.090
 R8B  C6   H17  single    0.970  0.020  1.090
 R8B  C    H18  single    0.970  0.020  1.090
 R8B  C5   H19  single    0.970  0.020  1.090
 R8B  C5   H20  single    0.970  0.020  1.090
 R8B  O5   H21  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 R8B  C15  C17  O6   116.42  3.000
 R8B  O6   C17  O7   127.39  3.000
 R8B  C15  C17  O7   116.19  3.000
 R8B  C16  C15  C14  118.94  3.000
 R8B  C16  C15  C17  120.64  3.000
 R8B  C14  C15  C17  120.42  3.000
 R8B  H2   C14  C13  119.96  3.000
 R8B  H2   C14  C15  118.88  3.000
 R8B  C13  C14  C15  121.15  3.000
 R8B  H3   C13  C11  119.08  3.000
 R8B  H3   C13  C14  120.57  3.000
 R8B  C11  C13  C14  120.35  3.000
 R8B  C12  C11  C10  117.48  3.000
 R8B  C12  C11  C13  119.12  3.000
 R8B  C10  C11  C13  123.40  3.000
 R8B  H4   C10  C9   121.00  3.000
 R8B  H4   C10  C11  119.72  3.000
 R8B  C9   C10  C11  119.28  3.000
 R8B  H5   C9   C8   119.84  3.000
 R8B  H5   C9   C10  121.14  3.000
 R8B  C8   C9   C10  119.03  3.000
 R8B  H6   C16  C12  118.21  3.000
 R8B  H6   C16  C15  120.47  3.000
 R8B  C12  C16  C15  121.32  3.000
 R8B  N    C12  C16  118.65  3.000
 R8B  N    C12  C11  122.24  3.000
 R8B  C16  C12  C11  119.11  3.000
 R8B  C8   N    C12  118.80  3.000
 R8B  C7   C8   N    119.92  3.000
 R8B  C7   C8   C9   116.91  3.000
 R8B  N    C8   C9   123.17  3.000
 R8B  H8   C7   H7   105.90  3.000
 R8B  H8   C7   O3   112.17  3.000
 R8B  H7   C7   O3   110.88  3.000
 R8B  H8   C7   C8   107.87  3.000
 R8B  H7   C7   C8   108.61  3.000
 R8B  O3   C7   C8   111.20  3.000
 R8B  C2   O3   C7   113.91  3.000
 R8B  H9   C2   C3   108.38  3.000
 R8B  H9   C2   C1   108.06  3.000
 R8B  C3   C2   C1   110.68  3.000
 R8B  H9   C2   O3   110.45  3.000
 R8B  C3   C2   O3   108.22  3.000
 R8B  C1   C2   O3   111.02  3.000
 R8B  H10  C1   C    106.97  3.000
 R8B  H10  C1   O4   111.14  3.000
 R8B  C    C1   O4   109.31  3.000
 R8B  H10  C1   C2   108.82  3.000
 R8B  C    C1   C2   109.16  3.000
 R8B  O4   C1   C2   111.34  3.000
 R8B  H11  O4   C1   108.00  3.000
 R8B  H12  C3   C4   109.64  3.000
 R8B  H12  C3   O2   111.52  3.000
 R8B  C4   C3   O2   110.62  3.000
 R8B  H12  C3   C2   108.42  3.000
 R8B  O2   C3   C2   108.19  3.000
 R8B  C4   C3   C2   108.37  3.000
 R8B  H13  O2   C3   108.54  3.000
 R8B  H14  C4   O    110.23  3.000
 R8B  H14  C4   O1   104.99  3.000
 R8B  O    C4   O1   109.21  3.000
 R8B  H14  C4   C3   107.91  3.000
 R8B  O1   C4   C3   113.55  3.000
 R8B  O    C4   C3   110.77  3.000
 R8B  C6   O1   C4   117.52  3.000
 R8B  H17  C6   H16  108.45  3.000
 R8B  H17  C6   H15  107.87  3.000
 R8B  H16  C6   H15  108.41  3.000
 R8B  H17  C6   O1   113.14  3.000
 R8B  H16  C6   O1   112.36  3.000
 R8B  H15  C6   O1   106.42  3.000
 R8B  C    O    C4   113.02  3.000
 R8B  H18  C    C5   108.21  3.000
 R8B  H18  C    O    109.85  3.000
 R8B  C5   C    O    108.62  3.000
 R8B  H18  C    C1   106.64  3.000
 R8B  O    C    C1   111.08  3.000
 R8B  C5   C    C1   112.37  3.000
 R8B  H20  C5   H19  107.14  3.000
 R8B  H20  C5   O5   111.72  3.000
 R8B  H19  C5   O5   111.74  3.000
 R8B  H20  C5   C    109.69  3.000
 R8B  H19  C5   C    107.75  3.000
 R8B  O5   C5   C    108.71  3.000
 R8B  H21  O5   C5   108.08  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 R8B  CONST_01  C11  C13  C14  C15    0.00   0.0  0
 R8B  CONST_02  C11  C12  C16  C15    0.00   0.0  0
 R8B  CONST_03  N    C12  C16  C15  180.00   0.0  0
 R8B  CONST_04  C10  C11  C13  C14  180.00   0.0  0
 R8B  CONST_05  C12  C11  C13  C14    0.00   0.0  0
 R8B  CONST_06  C12  C16  C15  C14    0.00   0.0  0
 R8B  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 R8B  CONST_08  C9   C10  C11  C13  180.00   0.0  0
 R8B  CONST_09  C16  C12  C11  C13    0.00   0.0  0
 R8B  CONST_10  N    C12  C11  C13  180.00   0.0  0
 R8B  CONST_11  C8   C9   C10  C11    0.00   0.0  0
 R8B  CONST_12  C8   N    C12  C11    0.00   0.0  0
 R8B  CONST_13  C16  C12  C11  C10  180.00   0.0  0
 R8B  CONST_14  N    C12  C11  C10    0.00   0.0  0
 R8B  CONST_15  N    C8   C9   C10    0.00   0.0  0
 R8B  CONST_16  C12  C11  C10  C9     0.00   0.0  0
 R8B  CONST_17  C12  N    C8   C9     0.00   0.0  0
 R8B  CONST_18  C8   N    C12  C16  180.00   0.0  0
 R8B  CONST_19  C13  C14  C15  C17  180.00   0.0  0
 R8B  CONST_20  C12  C16  C15  C17  180.00   0.0  0
 R8B  CONST_21  C7   C8   C9   C10  180.00   0.0  0
 R8B  CONST_22  C7   C8   N    C12  180.00   0.0  0
 R8B  CONST_23  H3   C13  C14  C15  180.00   0.0  0
 R8B  CONST_24  H6   C16  C15  C14  180.00   0.0  0
 R8B  CONST_25  H4   C10  C11  C13    0.00   0.0  0
 R8B  CONST_26  H2   C14  C13  C11  180.00   0.0  0
 R8B  CONST_27  H5   C9   C10  C11  180.00   0.0  0
 R8B  Var_01    C14  C15  C17  O7    -1.00  30.0  2
 R8B  Var_02    O3   C7   C8   C9   179.40  30.0  2
 R8B  Var_03    H15  C6   O1   C4   173.60  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 R8B  chir_01  C2  C1  O3  C3  positiv
 R8B  chir_02  C1  O4  C   C2  negativ
 R8B  chir_03  C3  O2  C4  C2  negativ
 R8B  chir_04  C4  O   O1  C3  negativ
 R8B  chir_05  C   O   C5  C1  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 R8B  plan-1  C17  0.020
 R8B  plan-1  C15  0.020
 R8B  plan-1  C14  0.020
 R8B  plan-1  C13  0.020
 R8B  plan-1  C11  0.020
 R8B  plan-1  C10  0.020
 R8B  plan-1  C9   0.020
 R8B  plan-1  C16  0.020
 R8B  plan-1  C12  0.020
 R8B  plan-1  N    0.020
 R8B  plan-1  C8   0.020
 R8B  plan-1  C7   0.020
 R8B  plan-1  H2   0.020
 R8B  plan-1  H3   0.020
 R8B  plan-1  H4   0.020
 R8B  plan-1  H5   0.020
 R8B  plan-1  H6   0.020
 R8B  plan-2  O7   0.020
 R8B  plan-2  C17  0.020
 R8B  plan-2  O6   0.020
 R8B  plan-2  C15  0.020

